diff --git a/Modules/PhotoacousticsLib/files.cmake b/Modules/PhotoacousticsLib/files.cmake index 40ceecd2a4..9452595421 100644 --- a/Modules/PhotoacousticsLib/files.cmake +++ b/Modules/PhotoacousticsLib/files.cmake @@ -1,57 +1,58 @@ SET(H_FILES include/mitkPAPropertyCalculator.h include/mitkPAVector.h include/mitkPATissueGeneratorParameters.h include/mitkPAInSilicoTissueVolume.h include/mitkPATissueGenerator.h include/mitkPAVesselTree.h include/mitkPAVessel.h include/mitkPAVesselMeanderStrategy.h include/mitkPANoiseGenerator.h include/mitkPAVolume.h include/mitkPAComposedVolume.h include/mitkPASlicedVolumeGenerator.h include/mitkPAProbe.h include/mitkPALightSource.h include/mitkPAIOUtil.h include/mitkPAMonteCarloThreadHandler.h include/mitkPASimulationBatchGenerator.h include/mitkPAFluenceYOffsetPair.h include/mitkPAVolumeManipulator.h include/mitkPAVesselProperties.h include/mitkPASimulationBatchGeneratorParameters.h include/mitkPAExceptions.h include/mitkPASpectralUnmixingFilterBase.h include/mitkPALinearSpectralUnmixingFilter.h + include/mitkPASpectralUnmixingSO2.h ) set(CPP_FILES Domain/Vessel/mitkPAVesselTree.cpp Domain/Vessel/mitkPAVessel.cpp Domain/Vessel/mitkPAVesselMeanderStrategy.cpp Domain/Vessel/mitkPAVesselProperties.cpp Domain/Volume/mitkPAInSilicoTissueVolume.cpp Domain/Volume/mitkPAVolume.cpp Domain/Volume/mitkPAComposedVolume.cpp Domain/Volume/mitkPAFluenceYOffsetPair.cpp Generator/mitkPATissueGenerator.cpp Generator/mitkPANoiseGenerator.cpp Generator/mitkPASlicedVolumeGenerator.cpp Generator/mitkPASimulationBatchGenerator.cpp Generator/mitkPASimulationBatchGeneratorParameters.cpp IO/mitkPAIOUtil.cpp Utils/mitkPAPropertyCalculator.cpp Utils/mitkPAVector.cpp Utils/mitkPATissueGeneratorParameters.cpp Utils/mitkPAVolumeManipulator.cpp Utils/ProbeDesign/mitkPAProbe.cpp Utils/ProbeDesign/mitkPALightSource.cpp Utils/Thread/mitkPAMonteCarloThreadHandler.cpp SUFilter/mitkPASpectralUnmixingFilterBase.cpp SUFilter/mitkPALinearSpectralUnmixingFilter.cpp - + SUFilter/mitkPASpectralUnmixingSO2.cpp ) set(RESOURCE_FILES spectralLIB.dat ) diff --git a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingSO2.h b/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingSO2.h new file mode 100644 index 0000000000..b5be263b95 --- /dev/null +++ b/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingSO2.h @@ -0,0 +1,50 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#ifndef MITKPHOTOACOUSTICSPECTRALUNMIXINGSO2_H +#define MITKPHOTOACOUSTICSPECTRALUNMIXINGSO2_H + +#include "mitkImageToImageFilter.h" +#include + +//Includes for smart pointer usage +#include "mitkCommon.h" +#include "itkLightObject.h" + + +namespace mitk { + namespace pa { + class MITKPHOTOACOUSTICSLIB_EXPORT SpectralUnmixingSO2 : public mitk::ImageToImageFilter + { + public: + + mitkClassMacro(SpectralUnmixingSO2, mitk::ImageToImageFilter) + + protected: + SpectralUnmixingSO2(); + virtual ~SpectralUnmixingSO2(); + + + private: + + virtual void GenerateData() override; + virtual void InitializeOutputs(); + virtual void CheckPreConditions(mitk::Image::Pointer inputHbO2, mitk::Image::Pointer inputHb); + float calculateSO2(float pixelHb, float pixelHbO2); + }; + } +} +#endif // MITKPHOTOACOUSTICSPECTRALUNMIXINGSO2_ diff --git a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingSO2.cpp b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingSO2.cpp new file mode 100644 index 0000000000..609d433cdd --- /dev/null +++ b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingSO2.cpp @@ -0,0 +1,124 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#include "mitkPASpectralUnmixingSO2.h" + +// ImageAccessor +#include +#include + +mitk::pa::SpectralUnmixingSO2::SpectralUnmixingSO2() +{ + this->SetNumberOfIndexedOutputs(1); + this->SetNthOutput(0, mitk::Image::New()); +} + +mitk::pa::SpectralUnmixingSO2::~SpectralUnmixingSO2() +{ + +} + +void mitk::pa::SpectralUnmixingSO2::GenerateData() +{ + MITK_INFO << "GENERATING DATA.."; + + // Get input image + mitk::Image::Pointer inputHbO2 = GetInput(0); + mitk::Image::Pointer inputHb = GetInput(1); + + + unsigned int xDim = inputHbO2->GetDimensions()[0]; + unsigned int yDim = inputHbO2->GetDimensions()[1]; + unsigned int size = xDim * yDim; + + MITK_INFO << "x dimension: " << xDim; + MITK_INFO << "y dimension: " << yDim; + + InitializeOutputs(); + + // Copy input image into array + mitk::ImageReadAccessor readAccessHbO2(inputHbO2); + mitk::ImageReadAccessor readAccessHb(inputHb); + + const float* inputDataArrayHbO2 = ((const float*)readAccessHbO2.GetData()); + const float* inputDataArrayHb = ((const float*)readAccessHb.GetData()); + + CheckPreConditions(inputHbO2, inputHb); + + //loop over every pixel @ x,y plane + for (unsigned int x = 0; x < xDim; x++) + { + for (unsigned int y = 0; y < yDim; y++) + { + unsigned int pixelNumber = x * yDim + y; + float pixelHb = inputDataArrayHb[pixelNumber]; + float pixelHbO2 = inputDataArrayHbO2[pixelNumber]; + float resultSO2 = calculateSO2(pixelHb, pixelHbO2); + auto output = GetOutput(0); + mitk::ImageWriteAccessor writeOutput(output); + float* writeBuffer = (float *)writeOutput.GetData(); + writeBuffer[x*yDim + y] = resultSO2; + } + } + MITK_INFO << "GENERATING DATA...[DONE]"; +} + +void mitk::pa::SpectralUnmixingSO2::CheckPreConditions(mitk::Image::Pointer inputHbO2, mitk::Image::Pointer inputHb) +{ + unsigned int xDimHb = inputHb->GetDimensions()[0]; + unsigned int yDimHb = inputHb->GetDimensions()[1]; + unsigned int sizeHb = xDimHb * yDimHb; + + unsigned int xDimHbO2 = inputHbO2->GetDimensions()[0]; + unsigned int yDimHbO2 = inputHbO2->GetDimensions()[1]; + unsigned int sizeHbO2 = xDimHbO2 * yDimHbO2; + + if (sizeHb != sizeHbO2) + mitkThrow() << "SIZE ERROR!"; + + if (xDimHb != xDimHbO2 || yDimHb != yDimHbO2) + mitkThrow() << "DIMENTIONALITY ERROR!"; + + MITK_INFO << "CHECK PRECONDITIONS ...[DONE]"; +} + +void mitk::pa::SpectralUnmixingSO2::InitializeOutputs() +{ + unsigned int numberOfInputs = GetNumberOfIndexedInputs(); + unsigned int numberOfOutputs = GetNumberOfIndexedOutputs(); + MITK_INFO << "InputsSO2: " << numberOfInputs << " OutputsSO: " << numberOfOutputs; + + // Set dimensions (2) and pixel type (float) for output + mitk::PixelType pixelType = mitk::MakeScalarPixelType(); + const int NUMBER_OF_SPATIAL_DIMENSIONS = 2; + auto* dimensions = new unsigned int[NUMBER_OF_SPATIAL_DIMENSIONS]; + for(unsigned int dimIdx=0; dimIdxGetDimensions()[dimIdx]; + } + + // Initialize numberOfOutput pictures with pixel type and dimensions + for (unsigned int outputIdx = 0; outputIdx < numberOfOutputs; outputIdx++) + { + GetOutput(outputIdx)->Initialize(pixelType, NUMBER_OF_SPATIAL_DIMENSIONS, dimensions); + } +} + +float mitk::pa::SpectralUnmixingSO2::calculateSO2(float Hb, float HbO2) +{ + float result = HbO2 / (Hb + HbO2); + return result; +} diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixing.cpp b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixing.cpp index aef2ca9882..c62c2ea1c9 100644 --- a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixing.cpp +++ b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixing.cpp @@ -1,226 +1,258 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include // Qmitk #include "SpectralUnmixing.h" // Qt #include // mitk image #include // Include to perform Spectral Unmixing #include "mitkPASpectralUnmixingFilterBase.h" #include "mitkPALinearSpectralUnmixingFilter.h" - +#include "mitkPASpectralUnmixingSO2.h" const std::string SpectralUnmixing::VIEW_ID = "org.mitk.views.spectralunmixing"; void SpectralUnmixing::SetFocus() { m_Controls.buttonPerformImageProcessing->setFocus(); } void SpectralUnmixing::CreateQtPartControl(QWidget *parent) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); connect(m_Controls.buttonPerformImageProcessing, &QPushButton::clicked, this, &SpectralUnmixing::DoImageProcessing); connect(m_Controls.ButtonAddWavelength, &QPushButton::clicked, this, &SpectralUnmixing::Wavelength); connect(m_Controls.ButtonClearWavelength, &QPushButton::clicked, this, &SpectralUnmixing::ClearWavelength); } // Adds Wavelength @ Plugin with button void SpectralUnmixing::Wavelength() { if (m_Wavelengths.empty()) { size = 0; } unsigned int wavelength = m_Controls.spinBoxAddWavelength->value(); m_Wavelengths.push_back(wavelength); size += 1; // size implemented like this because '.size' is const MITK_INFO << "ALL WAVELENGTHS: "; for (int i = 0; i < size; ++i) { MITK_INFO << m_Wavelengths[i] << "nm"; } } void SpectralUnmixing::ClearWavelength() { m_Wavelengths.clear(); } void SpectralUnmixing::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/, const QList &nodes) { // iterate all selected objects, adjust warning visibility foreach (mitk::DataNode::Pointer node, nodes) { if (node.IsNotNull() && dynamic_cast(node->GetData())) { m_Controls.labelWarning->setVisible(false); m_Controls.buttonPerformImageProcessing->setEnabled(true); return; } } m_Controls.labelWarning->setVisible(true); m_Controls.buttonPerformImageProcessing->setEnabled(false); } void SpectralUnmixing::DoImageProcessing() { QList nodes = this->GetDataManagerSelection(); if (nodes.empty()) return; mitk::DataNode *node = nodes.front(); if (!node) { // Nothing selected. Inform the user and return QMessageBox::information(nullptr, "Template", "Please load and select an image before starting image processing."); return; } // here we have a valid mitk::DataNode // a node itself is not very useful, we need its data item (the image) mitk::BaseData *data = node->GetData(); if (data) { // test if this data item is an image or not (could also be a surface or something totally different) mitk::Image *image = dynamic_cast(data); if (image) { std::stringstream message; std::string name; message << "PERFORMING SPECTRAL UNMIXING "; if (node->GetName(name)) { // a property called "name" was found for this DataNode message << "'" << name << "'"; } message << "."; MITK_INFO << message.str(); auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New(); m_SpectralUnmixingFilter->SetInput(image); // Set Algortihm to filter auto qs = m_Controls.QComboBoxAlgorithm->currentText(); std::string Algorithm = qs.toUtf8().constData(); if (Algorithm == "householderQr") m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::householderQr); else if (Algorithm == "ldlt") m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::ldlt); else if (Algorithm == "llt") m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::llt); else if (Algorithm == "colPivHouseholderQr") m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::colPivHouseholderQr); else if (Algorithm == "jacobiSvd") m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::jacobiSvd); else if (Algorithm == "fullPivLu") m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::fullPivLu); else if (Algorithm == "fullPivHouseholderQr") m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::fullPivHouseholderQr); else if (Algorithm == "test") m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::test); else mitkThrow() << "ALGORITHM ERROR!"; // Wavelength implementation into filter for (unsigned int imageIndex = 0; imageIndex < m_Wavelengths.size(); imageIndex++) { unsigned int wavelength = m_Wavelengths[imageIndex]; m_SpectralUnmixingFilter->AddWavelength(wavelength); } // Checking which chromophores wanted for SU if none throw exeption! unsigned int numberofChromophores = 0; DeOxbool = m_Controls.checkBoxDeOx->isChecked(); Oxbool = m_Controls.checkBoxOx->isChecked(); if (DeOxbool || Oxbool) { MITK_INFO << "CHOSEN CHROMOPHORES:"; } if (Oxbool) { numberofChromophores += 1; MITK_INFO << "- Oxyhemoglobin"; // Set chromophore Oxyhemoglobon: m_SpectralUnmixingFilter->AddChromophore( mitk::pa::SpectralUnmixingFilterBase::ChromophoreType::OXYGENATED_HEMOGLOBIN); } if (DeOxbool) { numberofChromophores += 1; MITK_INFO << "- Deoxygenated hemoglobin"; // Set chromophore Deoxygenated hemoglobin: m_SpectralUnmixingFilter->AddChromophore( mitk::pa::SpectralUnmixingFilterBase::ChromophoreType::DEOXYGENATED_HEMOGLOBIN); } if (numberofChromophores == 0) { mitkThrow() << "PRESS 'IGNORE' AND CHOOSE A CHROMOPHORE!"; } MITK_INFO << "Updating Filter..."; m_SpectralUnmixingFilter->Update(); if (Oxbool) { mitk::Image::Pointer HbO2 = m_SpectralUnmixingFilter->GetOutput(0); mitk::DataNode::Pointer dataNodeHbO2 = mitk::DataNode::New(); dataNodeHbO2->SetData(HbO2); dataNodeHbO2->SetName("HbO2"); this->GetDataStorage()->Add(dataNodeHbO2); } if (DeOxbool) { mitk::Image::Pointer Hb = m_SpectralUnmixingFilter->GetOutput(1); mitk::DataNode::Pointer dataNodeHb = mitk::DataNode::New(); dataNodeHb->SetData(Hb); dataNodeHb->SetName("Hb"); this->GetDataStorage()->Add(dataNodeHb); } mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(this->GetDataStorage()); + //*++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + //FRAGE zu SetInput: reicht es dort einen image pointer anzugeben? + bool sO2bool = m_Controls.checkBoxsO2->isChecked(); + if (sO2bool) + { + if (DeOxbool) + { + if (Oxbool) + { + MITK_INFO << "CALCULATE OXYGEN SATURATION ..."; + auto m_sO2 = mitk::pa::SpectralUnmixingSO2::New(); + m_sO2->SetInput(m_SpectralUnmixingFilter->GetOutput(0)); + m_sO2->SetInput(m_SpectralUnmixingFilter->GetOutput(1)); + m_sO2->Update(); + + mitk::Image::Pointer sO2 = m_sO2->GetOutput(0); + mitk::DataNode::Pointer dataNodesO2 = mitk::DataNode::New(); + dataNodesO2->SetData(sO2); + dataNodesO2->SetName("sO2"); + this->GetDataStorage()->Add(dataNodesO2); + + MITK_INFO << "[DONE]"; + } + else + mitkThrow() << "SELECT CHROMOPHORE OXYHEMOGLOBIN!"; + } + else + mitkThrow() << "SELECT CHROMOPHORE DEOXYHEMOGLOBIN!"; + } + mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(this->GetDataStorage()); + //*++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++/**/ + MITK_INFO << "Adding images to DataStorage...[DONE]"; } } } diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixingControls.ui b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixingControls.ui index db554dbecc..193c37365c 100644 --- a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixingControls.ui +++ b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixingControls.ui @@ -1,248 +1,268 @@ SpectralUnmixingControls 0 0 222 399 0 0 QmitkTemplate - - - - QLabel { color: rgb(255, 0, 0) } + + + + true - Please select an image! - - - - - - - Qt::Vertical + Deoxygenated hemoglobin - - - 20 - 40 - + + true - - - - - - Do image processing + + true - - Perform spectral unmixing + + false Oxyhemoglobin true - - - - true + + + + Do image processing - Deoxygenated hemoglobin + Perform spectral unmixing - - true + + + + + + Qt::Vertical - - true + + + 20 + 40 + - - false + + + + + + QLabel { color: rgb(255, 0, 0) } + + + Please select an image! Add Wavelength [nm] Qt::Vertical 2000 Clear all Wavelengths householderQr ldlt llt colPivHouseholderQr jacobiSvd fullPivLu fullPivHouseholderQr test Qt::Horizontal Qt::Horizontal 75 true Wavelengths settings Qt::Horizontal Qt::Horizontal 75 true Chromophore settings Qt::Horizontal 75 true Unmixing algorithm + + + + sO2 + + + + + + + + 75 + true + + + + Calculate oxygen saturation + + +